But just how diverse are some of the oldest living populations within Africa?

The authors discovered over 3.4 million genetic variants, or SNPs, of which a staggering 5-million of these variants are novel to us. Some of the loci give insight into adaptive changes in immunity, metabolism, olfactory and taste perception, reproduction, and wound healing. Interestingly, the Pygmy population, has multiple highly differentiated loci on genes on chromosome 3 which function in growth and anterior pituitary function and are associated with height.

We sequenced the whole genomes of five individuals in each of three different hunter-gatherer populations at >60× coverage and identify 13.4 million variants, substantially increasing the set of known human variation. We found evidence of archaic introgression in all three populations, and the distribution of time to most recent common ancestors from these regions is similar to that observed for introgressed regions in Europeans.

Of particular interest is that some of these SNPs aren’t found in any modern-day populations. This leads to the question if they originated due to ancient interbreeding between H. sapiens and an as-yet unidentified species of hominid. Lead author, Joseph Lachance, remarked how outstanding this is. Co-author Joshua Akey supports with,

Fossils degrade fast in Africa so we don’t have a reference genome for this ancestral lineage… one of the things we’re thinking is it could have been a sibling species to Neanderthals.

In the paper, the authors outline the great lengths they’ve taken show that the genetic traces resemble neither human nor Neanderthal DNA, and additionally document that none of the sequences taken from outside of Africa show any evidence of the foreign SNPs. All of which, has sparked Richard Klein to state that this conclusion to be as “irresponsible” particularly because there is no fossil evidence to support this mysterious sibling species.

Am I missing something? (Layperson here.) You write “Of particular interest is that some of these SNPs aren’t found in any modern-day populations”. But, then, how did we find them from taking samples of living people?

As to the irresponsibility of attributing unknown genes to a hypothetical sibling species to us and the Neanderthals and the Denisovans; given the probability of there being yet other undiscovered sibling species out there, it would be irresponsible not to suggest it.